8F6M: Pyruvate kinase PKM

Complex of Rabbit muscle pyruvate kinase with ADP and the phosphonate analogue of PEP mimicking the Michaelis complex. Determined by X-ray diffraction at 2.15 Å resolution. Released 24 May 2023.

Method: X-ray diffraction
Resolution: 2.15 Å
Organism: Oryctolagus cuniculus
Chains: 8
Atoms: 35,291
Mol. weight: 473.37 kDa
Ligands: GZ3, ALA, MN, SIN
Released: 24 May 2023

Explore 8F6M in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8F6M contains 205 α-helices and 220 β-strands across 8 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	25-30	6
β-strand	45-49	5	1
α-helix	57-66	10
β-strand	70-74	5	1
α-helix	80-95	16
β-strand	108-112	5	1
β-strand	118-119	2	2
β-strand	120	1	3
β-strand	123	1	4
β-strand	126	1	4
β-strand	131-133	3	5
α-helix	134	1
β-strand	138-142	5	2
α-helix	145-147	3
β-strand	151	1	4
β-strand	155-157	3	2
β-strand	158	1	3
α-helix	163-166	4
β-strand	172-175	4	2
β-strand	180-187	8	2
β-strand	191-196	6	2
β-strand	200-202	3	5
β-strand	207-209	3	2
α-helix	222-233	12
β-strand	238-241	4	1
α-helix	247-257	11
β-strand	265-270	6	1
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	1
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	1
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	1
α-helix	362-365	4
α-helix	370-386	17
α-helix	390-400	11
α-helix	407-421	15
β-strand	427-430	4	6
α-helix	435-442	8
β-strand	449-453	5	6
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	6
α-helix	476-478	3
α-helix	481-499	19
β-strand	507-512	6	6
β-strand	523-528	6	6

Chain B: 26 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	25-30	6
α-helix	37-39	3
β-strand	45-49	5	7
α-helix	57-66	10
β-strand	70-74	5	7
α-helix	80-95	16
β-strand	108-112	5	7
β-strand	118-119	2	8
β-strand	120	1	9
β-strand	123	1	10
β-strand	126	1	10
β-strand	131-133	3	11
α-helix	134	1
β-strand	138-142	5	8
α-helix	145-147	3
β-strand	151	1	10
β-strand	155-157	3	8
β-strand	158	1	9
α-helix	163-166	4
β-strand	172-175	4	8
β-strand	180-188	9	8
β-strand	191-196	6	8
β-strand	200-202	3	11
β-strand	207-209	3	8
α-helix	222-233	12
β-strand	238-241	4	7
α-helix	247-257	11
β-strand	265-270	6	7
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	7
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	7
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	7
α-helix	362-365	4
α-helix	370-387	18
α-helix	390-400	11
α-helix	407-421	15
β-strand	427-430	4	12
α-helix	435-442	8
β-strand	449-453	5	12
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	12
α-helix	476-478	3
α-helix	481-498	18
β-strand	507-512	6	12
β-strand	523-528	6	12

Chain C: 26 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	25-30	6
α-helix	37-39	3
β-strand	45-49	5	13
α-helix	57-66	10
β-strand	70-74	5	13
α-helix	80-95	16
β-strand	108-112	5	13
β-strand	118-119	2	14
β-strand	120	1	15
β-strand	123	1	16
β-strand	126	1	16
β-strand	131-133	3	17
α-helix	134	1
β-strand	138-142	5	14
α-helix	145-147	3
β-strand	151	1	16
β-strand	155-157	3	14
β-strand	158	1	15
α-helix	163-166	4
β-strand	172-175	4	14
β-strand	180-187	8	14
β-strand	191-196	6	14
β-strand	200-202	3	17
β-strand	207-209	3	14
α-helix	222-234	13
β-strand	238-241	4	13
α-helix	247-257	11
β-strand	265-270	6	13
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	13
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	13
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	13
α-helix	362-365	4
α-helix	370-387	18
α-helix	390-400	11
α-helix	407-421	15
β-strand	427-430	4	18
α-helix	435-442	8
β-strand	449-453	5	18
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	18
α-helix	476-478	3
α-helix	481-499	19
β-strand	507-512	6	18
β-strand	523-528	6	18

Chain D: 25 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	19
α-helix	17-20	4
α-helix	25-30	6
β-strand	37	1	19
α-helix	38-39	2
β-strand	45-49	5	20
α-helix	57-66	10
β-strand	70-74	5	20
α-helix	80-95	16
β-strand	108-112	5	20
β-strand	118-119	2	21
β-strand	120	1	22
β-strand	123	1	23
β-strand	126	1	23
β-strand	131-133	3	24
β-strand	138-142	5	21
α-helix	145-147	3
β-strand	151	1	23
β-strand	155-157	3	21
β-strand	158	1	22
α-helix	163-166	4
β-strand	172-175	4	21
β-strand	180-187	8	21
β-strand	191-196	6	21
β-strand	200-202	3	24
β-strand	207-209	3	21
α-helix	222-233	12
β-strand	238-241	4	20
α-helix	247-257	11
β-strand	265-270	6	20
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	20
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	20
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	20
α-helix	362-365	4
α-helix	370-386	17
α-helix	390-400	11
α-helix	407-422	16
β-strand	427-430	4	12
α-helix	435-442	8
β-strand	449-453	5	12
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	12
α-helix	476-478	3
α-helix	481-498	18
β-strand	507-512	6	12
β-strand	523-528	6	12

Chain E: 26 helices, 28 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	25-30	6
α-helix	37-39	3
β-strand	45-49	5	25
α-helix	57-66	10
β-strand	70-74	5	25
α-helix	80-95	16
β-strand	108-112	5	25
β-strand	119	1	26
β-strand	120	1	27
β-strand	123	1	28
β-strand	126	1	28
β-strand	131-133	3	29
α-helix	134	1
β-strand	138-142	5	2
α-helix	145-147	3
β-strand	151	1	28
β-strand	155-157	3	2
β-strand	158	1	27
α-helix	163-166	4
β-strand	172-175	4	2
β-strand	180-187	8	2
β-strand	191-198	8	2
β-strand	200-202	3	29
β-strand	207	1	26
β-strand	208-209	2	2
α-helix	222-233	12
β-strand	238-241	4	25
α-helix	247-257	11
β-strand	265-270	6	25
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	25
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	25
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	25
α-helix	362-365	4
α-helix	370-386	17
α-helix	390-400	11
α-helix	407-421	15
β-strand	427-430	4	18
α-helix	435-442	8
β-strand	449-453	5	18
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	18
α-helix	476-478	3
α-helix	481-498	18
β-strand	507-512	6	18
β-strand	523-528	6	18

Chain F: 25 helices, 27 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	25-30	6
α-helix	37-39	3
β-strand	45-49	5	30
α-helix	57-66	10
β-strand	70-74	5	30
α-helix	80-95	16
β-strand	108-112	5	30
β-strand	119	1	31
β-strand	120	1	32
β-strand	123	1	33
β-strand	131-133	3	34
β-strand	138-142	5	35
α-helix	145-147	3
β-strand	151	1	33
β-strand	155-157	3	35
β-strand	158	1	32
α-helix	163-166	4
β-strand	172-175	4	35
β-strand	180-187	8	35
β-strand	191-196	6	35
β-strand	200-202	3	34
β-strand	207	1	31
β-strand	208-209	2	35
α-helix	222-233	12
β-strand	238-241	4	30
α-helix	247-257	11
β-strand	265-270	6	30
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	30
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	30
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	30
α-helix	362-365	4
α-helix	370-387	18
α-helix	390-400	11
α-helix	407-422	16
β-strand	427-430	4	6
α-helix	435-442	8
β-strand	449-453	5	6
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	6
α-helix	476-478	3
α-helix	481-499	19
β-strand	507-512	6	6
β-strand	523-528	6	6

Chain G: 26 helices, 25 β-strands

Element	Residues	Length	Sheet
α-helix	17-20	4
α-helix	25-30	6
α-helix	37-39	3
β-strand	45-49	5	36
α-helix	57-66	10
β-strand	70-74	5	36
α-helix	80-95	16
α-helix	104-106	3
β-strand	108-112	5	36
β-strand	119	1	37
β-strand	120	1	38
β-strand	131-133	3	39
β-strand	138-142	5	40
α-helix	145-149	5
β-strand	155-157	3	40
β-strand	158	1	38
α-helix	163-165	3
β-strand	172-175	4	40
β-strand	180-184	5	40
β-strand	193-198	6	40
β-strand	200-202	3	39
β-strand	207	1	37
β-strand	208-209	2	40
α-helix	222-233	12
β-strand	238-241	4	36
α-helix	247-257	11
β-strand	265-270	6	36
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	36
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	36
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	36
α-helix	362-365	4
α-helix	370-386	17
α-helix	390-400	11
α-helix	407-422	16
β-strand	427-430	4	41
α-helix	435-442	8
β-strand	449-453	5	41
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	41
α-helix	476-478	3
α-helix	481-498	18
β-strand	507-512	6	41
β-strand	523-528	6	41

Chain H: 26 helices, 30 β-strands

Element	Residues	Length	Sheet
β-strand	14	1	42
α-helix	17-20	4
α-helix	25-30	6
β-strand	37	1	42
α-helix	38-39	2
β-strand	45-49	5	43
α-helix	57-66	10
β-strand	70-74	5	43
α-helix	80-95	16
β-strand	108-112	5	43
β-strand	119	1	44
β-strand	120	1	45
β-strand	123	1	46
β-strand	126	1	46
β-strand	131-133	3	47
α-helix	134	1
β-strand	138-142	5	21
α-helix	145-147	3
β-strand	151	1	46
β-strand	155-157	3	21
β-strand	158	1	45
α-helix	163-166	4
β-strand	172-175	4	21
β-strand	180-187	8	21
β-strand	191-198	8	21
β-strand	200-202	3	47
β-strand	207	1	44
β-strand	208-209	2	21
α-helix	222-233	12
β-strand	238-241	4	43
α-helix	247-257	11
β-strand	265-270	6	43
α-helix	273-277	5
α-helix	279-285	7
β-strand	288-292	5	43
α-helix	293-299	7
α-helix	302-304	3
α-helix	305-319	15
β-strand	323-326	4	43
α-helix	331-334	4
α-helix	341-353	13
β-strand	357-360	4	43
α-helix	362-365	4
α-helix	370-386	17
α-helix	390-400	11
α-helix	407-421	15
β-strand	427-430	4	41
α-helix	435-442	8
β-strand	449-453	5	41
α-helix	456-461	6
α-helix	462-464	3
β-strand	468-472	5	41
α-helix	476-478	3
α-helix	481-499	19
β-strand	507-512	6	41
β-strand	523-528	6	41

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Pyruvate kinase PKM	A, B, C, D, E, F, G, H	protein	531	Oryctolagus cuniculus	P11974 (AlphaFold model)

Sequence of entity 1 (A, B, C, D, E, F, G, H), FASTA

>8F6M_1 Pyruvate kinase PKM (chains A, B, C, D, E, F, G, H)
MSKSHSEAGSAFIQTQQLHAAMADTFLEHMCRLDIDSAPITARNTGIICTIGPASRSVET
LKEMIKSGMNVARMNFSHGTHEYHAETIKNVRTATESFASDPILYRPVAVALDTKGPEIR
TGLIKGSGTAEVELKKGATLKITLDNAYMEKCDENILWLDYKNICKVVDVGSKVYVDDGL
ISLQVKQKGPDFLVTEVENGGFLGSKKGVNLPGAAVDLPAVSEKDIQDLKFGVEQDVDMV
FASFIRKAADVHEVRKILGEKGKNIKIISKIENHEGVRRFDEILEASDGIMVARGDLGIE
IPAEKVFLAQKMIIGRCNRAGKPVICATQMLESMIKKPRPTRAEGSDVANAVLDGADCIM
LSGETAKGDYPLEAVRMQHLIAREAEAAMFHRKLFEELARASSHSTDLMEAMAMGSVEAS
YKCLAAALIVLTESGRSAHQVARYRPRAPIIAVTRNHQTARQAHLYRGIFPVVCKDPVQE
AWAEDVDLRVNLAMNVGKARGFFKKGDVVIVLTGWRPGSGFTNTMRVVPVP

Ligands and cofactors

ID	Name	Formula	Copies
GZ3	(e)-2-methyl-3-phosphonoacrylate	C4 H7 O5 P	4
ALA	Alanine	C3 H7 N O2	8
MN	Manganese (II) ion	Mn	15
SIN	Succinic acid	C4 H6 O4	12
ADP	Adenosine-5'-diphosphate	C10 H15 N5 O10 P2	5

Water and common crystallization additives (GOL, K) are not listed.

Primary citation

PYK-SubstitutionOME: an integrated database containing allosteric coupling, ligand affinity and mutational, structural, pathological, bioinformatic and computational information about pyruvate kinase isozymes. Swint-Kruse, L., Dougherty, L.L., Page, B. et al. Database (Oxford) (2023) 2023. DOI 10.1093/database/baad030 · PubMed

Other PDB entries of the same protein (UniProt P11974 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2G50 1.65 Å, The location of the allosteric amino acid binding site of muscle pyruvate kinase.
1A49 2.1 Å, Bis MG-ATP-K-oxalate complex of pyruvate kinase
7R6Y 2.25 Å, E117K mutant pyruvate kinase from rabbit muscle
8F5U 2.3 Å, Rabbit muscle pyruvate kinase in complex with magnesium, potassium and pyruvate
1A5U 2.35 Å, Pyruvate kinase complex with bis MG-ATP-na-oxalate
3N25 2.41 Å, The structure of muscle pyruvate kinase in complex with proline, pyruvate, and Mn2+
8F5T 2.41 Å, Rabbit muscle pyruvate kinase in complex with sodium and magnesium
1AQF 2.7 Å, Pyruvate kinase from rabbit muscle with MG, K, and L-phospholactate
1F3X 2.8 Å, S402P mutant of rabbit muscle pyruvate kinase
1PKN 2.9 Å, Structure of rabbit muscle pyruvate kinase complexed with MN2+, K+, and pyruvate
1F3W 3.0 Å, Recombinant rabbit muscle pyruvate kinase

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